Biochemistry I

Fall 2007, Chem 4400, Dr. Koni Stone, N103, 10:10-11:08

Office:
N 358, 667-3570, koni@chem.csustan.edu

Office hours:
W,F: 11:15-12:15,

T,R: 1-2 and by appointment

Text:
Lehninger Principles of Biochemistry by David Nelson and Michael Cox, 4th  Edition, Worth Publishers, 2004.

Web page for the class: http://science.csustan.edu/stone/chem4400/4400main.htm
Welcome to the first semester of a full year course in Biochemistry. You must have taken and passed (a C or better is highly recommended) 2 semesters of Organic chemistry in order to register for this course.

The learning goals for this class are:
1. Learn biochemical facts, including the language used to describe biochemistry and the methods used to study it.
2. Gain an understanding of some biochemical principles including
  • Acid base chemistry and buffers
  • Amino acids, peptides and proteins
  • Protein structure and the relationship between structure and function
  • Enzyme kinetics and mechanisms
  • Regulation of biochemical reactions
  • Biomolecules such lipids, carbohydrates and nucleic acids
  • Biomembrane structure and function

3. Improve writing skills and learn how to find and use resources to answer questions.
4. Learn how to work with others as a member of a team.

The following devices will be used to assess your learning in this class.

Device

Dates

Points

Percent of total points

Exams

September 28, October 26th, and December 7. There are no make-up exams, please plan accordingly.

300

37.5

Quizzes, Assignments and Activities

Any day except exam days (actual points will be normalized to 100 points)

100

12.5

Service learning

Selection of option: Oct. 3

Mid term summary or experiment handout: Oct 29

Final report due December 10, 2007

10

30

60

12.5

Comprehensive Final Exam

Monday, December 17, 2007, 8:30- 10:30

200

25

Literature reports

Due dates:

September  26,  (Structure 10 points)

October 5 (Brief summary 15 points)
October 31 (1st draft  of  drug mechanism of action 25 points)
November 26 (Final draft 50 points)

100

12.5

This course is graded with letter grades using the following minimum scores:
A, 90%; B, 80%; C, 70%; D, 60%.
The last day to withdraw from this course is Tuesday, October 2, 2007.

Quizzes and class activities will cover all information presented in class and all material in the required readings. These materials are designed to help you learn the material and determine your strengths and weaknesses. Some will be collected and graded.  Exam questions will be very similar to homework, quiz and activity questions. No make-up exams, quizzes or class activities will be given. If you have extenuating circumstances that involve serious and compelling reasons for missing class, you are advised to schedule a consultation with Dr. Stone as soon as possible, so that an appropriate plan of action can be developed.


The final exam will be comprehensive and will be based on questions that were on the quizzes, activities and exams.

Service based learning is a great way to gain a greater understanding of chemistry while having fun. You can choose from several options in order to fulfill this course requirement.

  1. Tutor a CHEM 2090 (Biochemistry for Nurses) or CHEM 1110 (General Chemistry) or CHEM 3010 (Organic I) student one hour a week for 9 weeks.  You will write a mid term summary of your experience that is due Oct 29th.  Include the name of the student that you are tutoring and a brief summary of when and where you meet and what topics you have helped the student learn.  
  2. Work in a group (minimum of 3, maximum of 5 students) to develop a science (Biochemistry related) activity to do with elementary students.  You pick and organize the activity, we pay for the supplies.  You may use a previously published activity or you may generate your own activity. Your group must rewrite the activity for the level of students that you will be working with.  These experiment handouts and a list of requested supplies and eqipment are due Oct 29th.  
    1. Fifth grade students, available dates: Fridays (1:00-3:00)  November 2, 9,16, 30 and December 7
    2. Third grade students, available dates: Thursdays (1:00-3:00) November 1, 8, 15, 29 and December 6
  3. Select a topic, write a 4-5 page paper and give a 15 minute presentation of your paper to the class. The topic must be submitted and approved by October 3rd, and a rough draft is due Oct 29th.  

After you have completed your service based learning activity, you will need to complete a written report. These reports are due December 10th.  Please include the following:

  • What activity did you select and why did you select it? 
  • Fully describe what you did. How did this activity enhance your understanding of chemistry? 
  • What advice do you have for future students that might select this activity?
Writing Assigment: 
       Each student will select a drug and then use this drug for the following assignments.  Once you have found your drug, let Dr. Stone know what it is by sending an email to koni@chem.csustan.edu.  Everyone will be using a different drug, so drugs that have already been selected will be listed on the web.

Assignment 1:  10 points, Due: September 26  
Draw the structure of your drug.  There is a free program called ISIS draw that is available at www.mdli.com, or you can draw it by hand.  Indicate all of the functional groups on your drug molecule.  Predict the water solubility of your drug.   Describe your rationale based on the functional groups that are present.   Look up the water solubility of your drug and compare it to your prediction.  

Assignment 2: 15 points, Due: October 5
Write a brief summary of how the drug is used.  What illness does it treat?  Who is affected by this illness?  Summarize the pharmaceutical importance of this drug.  Limit this summary to 2 typed, double spaced pages.  Fully cite all of your references, including titles, authors, dates, journal, volume and pages.  Do not use any online encyclopedias as references (sorry no wikipedia).  Also, do not use quotations.  Describe the drug’s use with your own words.

Assignment 3: 25 points, Due: October 31
Fully describe how the drug works.  You will need to explain the disease that is being treated in full biochemical detail.  Then, describe how the drug works at the molecular level.  Find at least two experiments in the literature that demonstrate the mechanism of action of the drug.  Describe how these experiments were done.  Fully cite all of your references, including titles, authors, dates, journal, volume and pages.  Do not use any online encyclopedias as references.   Also, do not use quotations. Describe the drug’s use with your own words.

Assignment 4: 50 points, Due: November 26
        Rewrite assignment 3 adding details and incorporating the feedback that you received from Assignment 3.  Also, include a brief biochemical discussion of the side effects and contraindications for your drug.  Fully cite all of your references, including titles, authors, dates, journal, volume and pages.  Do not use any online encyclopedias as references.  Also, do not use quotations.  Describe the drug’s use with your own words.

General Directions:

        These reports must be generated using a word processing computer program. No handwritten text, tables or graphics (except for the structure of the molecule) will be accepted. Please use double spacing and select a font that has 10-12 characters per inch. Both MacIntosh and IBM machines are available for your use in the computer labs in the Library building.  
        Fully cite all of your references, including titles, authors, dates, journal, volume and pages.  Do not use any online encyclopedias as references.  Also, do not use quotations.  Describe the drug’s use with your own words.
        The objectives of this assignment are to strengthen your literature research and writing skills. This will also give you the opportunity to learn about biochemical topics in more detail.  

Papers are due at the beginning of class on the above due dates. Late papers will be penalized 10% per 24 hour period. Papers will be graded on content, thoroughness, validity, clarity, organization, punctuation and grammar.
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Homework: Problems from the text will be assigned and some problems will be presented in class by students. Please consult the main page for this class.

Reading Schedule*

Week

Chapter

1

1: Intro,Cells, Biomolecules

2

2: Water

3

3: Amino acids, peptides and proteins

4

4: 3D Protein structure

5

5: Protein function 

6

6:  Enzymes

7

6:  Enzymes

8

7: Carbohydrates and glycobiology

9

8:  Nucleotides and nucleic acids

10

9:  DNA based information technologies

11

10: Lipids

12

11: Biological membranes and transport
*Other supplemental reading material may be assigned
Note: This syllabus is intended to be used as a guide, it is not a legal contract. This syllabus may change, depending upon circumstances.

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